3CY5 | pdb_00003cy5

Crystal structure determination of buffalo (Bubalus bubalis) hemoglobin at 2 angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb3CY5/pdb

• Classification: Oxygen storage, Oxygen transport
• Organism(s): Bubalus bubalis
• Mutation(s): No 


• Deposited: 2008-04-25 Released: 2009-04-28 
• Deposition Author(s): Balasubramanian, M., Sathya Moorthy, P., Neelagandan, K., Ponnuswamy, M.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.270 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.193 (Depositor) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Crystal structure determination of hemoglobin from Buffalo (Bubalus bubalis) at 2 angstrom resolution

Balasubramanian, M., Sathya Moorthy, P., Neelagandan, K., Ponnuswamy, M.N.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Dihedral - D2  (Explore in 3D)
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 64.64 kDa 
• Atom Count: 4,871 
• Modeled Residue Count: 572 
• Deposited Residue Count: 572 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit alpha-2	A, C	141	Bubalus bubalis	Mutation(s): 0
UniProt
Find proteins for Q9TSN8 (Bubalus bubalis) Explore Q9TSN8  Go to UniProtKB:  Q9TSN8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit beta	B, D	145	Bubalus bubalis	Mutation(s): 0
UniProt
Find proteins for P67820 (Bubalus bubalis) Explore P67820  Go to UniProtKB:  P67820

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	E [auth A], F [auth B], G [auth C], H [auth D]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.270 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.193 (Depositor) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.064	α = 90
b = 74.677	β = 90
c = 110.224	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-28 
Deposition Author(s): Balasubramanian, M., Sathya Moorthy, P., Neelagandan, K., Ponnuswamy, M.N.

Revision History  

• Version 1.0: 2009-04-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2016-12-21
  Changes: Other
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description